Filers apparently can still use the IRS site to pay via a debit or credit card; however, you'll be on the hook for fees ranging from $2 to $3.95 for debit transactions and expenses approaching 2 percent for credit card payments.

Don't forget: You can also still pay what you owe with a paper check.

"Currently, certain IRS systems are experiencing technical difficulties," an IRS spokeswoman wrote in an e-mail to CNBC. "Taxpayers should continue filing their tax returns as they normally would." The spokeswoman didn't say when the system went down.

IRS Acting Commissioner David J. Kautter told The Washington Post that filers wouldn't be penalized if their returns were late due to the site's problems. Normally, you're liable for penalties if you fail to file your return and pay your taxes in a timely fashion.

"We understand that the IRS is experiencing technical difficulties today with the transmission of direct tax return payments," said Richard Neal, D-Mass., the ranking member of the House Ways and Means Committee.

"Given this news, I hope that the IRS will make accommodations so that every taxpayer attempting to file today has a fair shot to do so without penalty," he said.

A spokesperson at commercial tax preparer TurboTax said that the IRS's technical difficulties affects all tax preparers and tax returns.

"Taxpayers should go ahead and continue to prepare and file their taxes as normal with TurboTax," the spokesperson said.

"TurboTax has uninterrupted service and is available and accepting e-filed returns," she said. "We will hold returns until the IRS is ready to begin accepting them again."

H&R Block said it will continue to accept returns from filers.

"Despite the IRS outage, H&R Block is open and continuing to process tax returns for our clients," said an H&R Block spokesperson.

"While the IRS system is down, we are completing the returns, which will be sent as soon as the IRS system re-opens and will be considered filed on time."

New York State tax app crashes briefly

On Tuesday morning, the New York State Tax Department also announced on its Twitter page that its Personal Income Tax Extension web app was experiencing system problems. New York State Tax Department's Tweet

Just prior to noon, the department announced access to its application was restored.

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